Following an issue with my kubuntu installation (graphics driver libraries problem), I decided to restore a backup of my system that I had made several weeks earlier, but since I didn't want to lose all the settings and other customizations, I copied my home folder but with root permissions because I couldn't mount my backup disk as simple user.
I just had an issue where users were directly added to the ACL of a folder. I created a group, added them to the group, added the group to the ACL of the folder and then removed the users and pressed apply. 18 of about 20 users were unaffected, but for some reason two users were denied access. I check the effective permissions tab and they were there. I added both users explicitly again.